Variant report

Variant	rs13125511
Chromosome Location	chr4:48484887-48484888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:48484883-48485759	H1-neurons	neurons:	n/a	n/a
2	KAP1	chr4:48484776-48485061	HEK293	kidney:	n/a	n/a
3	EP300	chr4:48484227-48486994	SK-N-SH	brain:	n/a	chr4:48485456-48485472 chr4:48485429-48485438 chr4:48485459-48485475 chr4:48484359-48484368 chr4:48485366-48485382
4	MAZ	chr4:48484876-48485582	K562	blood:	n/a	chr4:48485105-48485115
5	REST	chr4:48484690-48486047	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48484114..48487251-chr4:48504187..48509460,5	K562	blood:
2	chr4:48341909..48343469-chr4:48483589..48486077,2	K562	blood:

Variant related genes	Relation type
SLC10A4	TF binding region
ENSG00000109171	Chromatin interaction
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10031120	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10938532	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10938533	0.81[ASN][1000 genomes]
rs13105691	0.82[EUR][1000 genomes]
rs13145421	0.82[EUR][1000 genomes]
rs17472113	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17655898	0.82[EUR][1000 genomes]
rs4413478	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812622	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6827019	0.93[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7340880	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7668401	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7694862	0.89[ASN][1000 genomes]
rs9993088	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv879008	chr4:48473439-48496804	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv879009	chr4:48476539-48494546	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3421012	chr4:48483395-48487593	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48484600-48485000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
2	chr4:48484600-48485000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
3	chr4:48484600-48485000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
4	chr4:48484600-48485000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
5	chr4:48484600-48485000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:48484600-48485200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
7	chr4:48484600-48485200	Flanking Active TSS	K562	blood
8	chr4:48484600-48486600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr4:48484600-48486600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr4:48484800-48485000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
11	chr4:48484800-48485000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:48484800-48485000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:48484800-48485000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr4:48484800-48485000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr4:48484800-48485000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:48484800-48485000	Enhancers	Brain Substantia Nigra	brain
17	chr4:48484800-48485000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr4:48484800-48485000	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr4:48484800-48485200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
20	chr4:48484800-48485200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
21	chr4:48484800-48485200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr4:48484800-48485200	Bivalent Enhancer	Fetal Brain Male	brain
23	chr4:48484800-48485200	Bivalent Enhancer	Fetal Heart	heart
24	chr4:48484800-48485800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:48484800-48485800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:48484800-48486000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:48484800-48486000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:48484800-48486200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
29	chr4:48484800-48486600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:48484800-48487200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
31	chr4:48484800-48487200	Active TSS	A549	lung

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